Contacts of the strand formed by residues 257 - 265 (chain C) in PDB entry 2J2M
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 257 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C ARG 5.5 0.3 - - - +
219C PRO* 3.8 1.0 - - - +
220C LYS* 3.0 62.4 + - + +
221C GLU* 4.7 3.7 + - - +
255C PHE* 3.4 17.5 + - - +
256C PRO* 1.3 74.1 - - - +
258C TRP* 1.3 72.7 + - - +
296C THR* 4.5 9.8 + - - +
297C MET 3.0 10.8 - - - +
298C THR* 3.3 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C PHE* 3.6 22.9 - + - -
113C PHE* 3.5 22.0 - + - -
190C TYR 3.2 24.7 - - - -
191C ARG* 3.8 11.9 - - + -
193C MET 2.7 22.8 + - - -
217C TRP* 3.5 21.1 - - + -
218C VAL 3.0 14.1 - - - +
219C PRO* 3.4 27.2 - - + +
220C LYS* 4.5 0.7 - - - +
246C THR* 5.9 0.9 - - + -
256C PRO* 3.5 34.5 - - + -
257C GLU* 1.3 82.9 - - - +
259C ASP* 1.3 62.4 + - - +
296C THR* 3.3 4.4 - - - -
297C MET* 2.8 47.4 + - + +
299C LEU* 3.6 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ARG 3.4 3.8 - - - +
217C TRP* 3.4 2.4 - - - -
218C VAL* 2.9 35.8 + - + +
220C LYS* 6.0 3.1 - - - +
258C TRP* 1.3 74.6 - - - +
260C LEU* 1.3 59.9 + - - +
261C PHE* 3.7 21.4 - - + -
293C HIS* 2.9 29.4 + - - +
295C GLY 3.4 1.3 - - - -
296C THR* 3.1 23.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PHE* 3.5 31.6 - - + -
80C PHE* 6.2 0.2 - - + -
81C LEU* 5.9 1.1 - - + -
117C PHE* 5.1 2.2 - - + -
124C TRP* 5.1 12.6 - - + -
126C PHE* 5.4 0.7 - - + -
203C TRP* 6.2 1.1 - - + -
215C LEU* 3.8 30.1 - - + -
216C ARG 3.2 19.1 - - - +
217C TRP* 3.6 41.9 - - + +
258C TRP 4.1 0.2 + - - -
259C ASP* 1.3 73.1 - - - +
261C PHE* 1.3 60.4 + - - +
293C HIS* 3.8 2.4 - - - -
294C VAL* 2.8 49.6 + - + +
295C GLY 2.8 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C LEU* 3.5 6.8 - - - +
216C ARG* 2.8 43.4 + - + +
218C VAL* 3.7 31.2 - - + -
259C ASP* 3.7 25.8 - - + -
260C LEU* 1.3 76.0 - - - +
262C VAL* 1.3 59.4 + - - +
291C PHE* 3.6 34.8 - + + -
292C GLN 3.2 8.3 - - - +
293C HIS* 3.4 45.3 - + + -
294C VAL* 4.2 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C MET* 4.2 15.9 - - - -
75C TYR* 5.1 1.1 - - + -
203C TRP* 4.1 11.7 - - + -
213C ILE* 3.5 30.3 - - + -
214C LYS 3.3 10.3 - - - +
215C LEU* 3.8 13.9 - - + -
261C PHE* 1.3 75.8 - - - +
263C GLN* 1.3 68.6 + - - +
264C VAL* 4.2 10.8 - - + -
290C PRO 3.6 2.6 - - - +
292C GLN* 2.9 50.4 + - + +
294C VAL* 3.8 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C TYR 3.6 0.2 - - - +
213C ILE* 3.0 10.9 - - - +
214C LYS* 2.9 39.2 + - - +
216C ARG* 2.6 32.9 + - + -
262C VAL* 1.3 73.9 - - - +
264C VAL* 1.3 61.4 + - - +
284C TRP* 2.8 47.7 + - + +
285C PHE 3.8 0.6 + - - -
289C ILE* 2.6 27.2 + - + +
290C PRO 3.5 17.0 - - - +
291C PHE* 3.4 25.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C TYR* 3.8 40.8 - - + +
211C VAL* 3.8 25.4 - - + -
212C TYR 3.5 2.0 - - - -
213C ILE* 4.3 4.9 - - + -
262C VAL* 4.2 15.5 + - + -
263C GLN* 1.3 77.8 - - - +
265C LEU* 1.3 64.9 + - - +
266C ASP 4.3 0.9 - - - +
289C ILE* 3.3 20.3 - - - +
290C PRO 4.6 1.8 + - - -
292C GLN* 3.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C VAL* 3.7 5.0 - - - -
212C TYR* 2.8 43.9 + - + +
264C VAL* 1.3 75.6 - - - +
266C ASP* 1.3 78.2 + - - +
267C PRO 3.5 0.2 - - - -
269C ASP* 3.9 14.6 - - + +
270C VAL* 4.3 10.5 - - + -
273C PHE* 3.8 29.2 - - + -
277C PRO* 3.8 34.8 - - + -
284C TRP* 3.7 28.9 - - + -
289C ILE* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il